The Taman TAR wildlife sanctuary is home to two main species of monkey - the pig-tailed macaque and the more numerous long-tailed macaque - both protected by law.

"Macaques are prolific and able to reproduce very fast, so there is no question of the species being threatened into extinction through culling."

- Malaysian Wildlife Department

The cull has pitched the wildlife department against animal welfare groups and primate experts alarmed not only at the number of animals killed, but the way in which the cull was carried out. Activists say some monkeys are being shot as they sit in trees.

No recent scientific survey of the macaque population has been completed, critics say, and such an aggressive approach to controlling their numbers could push the species to the brink of extinction.

The wildlife department - known as Perhilitan - insists there is no such risk and the killing is necessary to deal with the rising incidence of human-monkey conflict.

"The culling was not done in haste, but in the best interests of the public," a government statement said. "Macaques are prolific and able to reproduce very fast, so there is no question of the species being threatened into extinction through culling."

Human encroachment

The past 30 years has seen rapid economic development across much of Southeast Asia, including Malaysia. Much of the monkeys' traditional forest habitat has been cleared to make way for factories, homes and plantations.

"Problems with macaques are generally a good measure of the overall severity of environmental problems and poor waste management," said Michael Gumert, an assistant professor at Singapore's Nanyang Technological University, whose work focuses on the region's macaque population.

"The first step needed is to get a trustworthy team to census the population. Without real scientific-based surveys, everything is guess work."

Perhilitan says an "inventory" of the macaque population took place in 2007, which showed there were 740,000 macaques across the peninsula. Depending on the availability of food and habitat, the animal population can expand by as much as seven percent each year, it said.

Scientists describe the macaque as an "edge" species because the monkeys like to live on the forest fringe, near rivers or along the coast, which gives the animal its other name, the crab-eating macaque.

They're known for being intelligent and inquisitive; the balcony doors of five star resorts from Langkawi to the east coast often come with warnings about the monkeys who keep a watchful eye on guests from the nearby treetops or, sometimes, the roof.

In housing areas closer to the forest, homeowners risk having their fridge raided if they leave doors or windows open, and monkeys have been known to snatch clothes and towels belonging to unsuspecting swimmers. Farmers have been forced to change crops and erect electric fences to keep the macaques out.

Conflicts with humans led to the mass cull [Getty Images]

In an incident that made headlines across the world, a new-born baby died after being snatched, and dropped, by a monkey in 2010.

'Indiscriminate butchery'?

Maketab Mohamed is president of the Malaysian Nature Society and director of Occupational Safety, Health and the Environment at Universiti Teknologi Malaysia (UTM) in the southern state of Johor. He said the campus has long been troubled by the presence of long-tailed macaques and has little sympathy for the animals.

"They raid garbage, raid the fruits clean off our fruit trees and even attack students," Maketab said in an email. "Personally, I will say I support the culling - and any critic is welcome to buy a house in a macaque-infested neighbourhood."

Animal rights groups say they have evidence that suggests the animals are trapped in cages, perhaps as many as 12 at a time, before they are shot. The pattern of wounding on the bodies also suggests the animals suffered before they died.

"Perhilitan does not have the resources to [humanely] carry out killing on such a scale," said N Surendran, president of animal rights group ROAR.

"The photos show that the monkeys were sometimes shot down from trees. That's not humane. This kind of indiscriminate butchery can have an impact on the survival of the species," Surendran said.

In a statement to Al Jazeera, Perhilitan stressed the killing was done humanely, and according to a plan that had been "deeply discussed with NGOs, experts and scientists". It acknowledged the cull could take place in a number of ways, including organised hunting expeditions.

"The objective is also to protect human safety [and] reduce economic losses due to damage done by wildlife to commercial crops and property," the statement said. "We have to see the bigger picture rather than just focusing on the numbers."

Kill quotas

Internal documents obtained by Al Jazeera show the department sets a kill quota for each state, and operates two incinerators to dispose of the bodies.

Selangor state had the largest quota of 16,500 animals killed, and had reached 96 percent of that target by the end of September, according to the official documents.

In the southern state of Johor, the cull had exceeded its target in the first nine months of the year, with 12,694 killed compared with its annual quota of 12,000.

The ministry of the environment denied there were any cull quotas.

The documents also show while monkeys were the source of many conflicts, the cost was negligible and there were few injuries caused. In fact, elephants were more costly and snakes more deadly. Moreover, official figures show complaints about monkeys have actually declined to 3,235 in 2012, compared with 4,193 back in 2005.

"We certainly have a great deal to learn about how to care for our natural environment, as well as the creatures we must learn to share it with."

- Susan Lau, resident

A special committee set up by Perhilitan to investigate the allegations made by the NGOs was due to report its findings to the ministry of the environment last week. The ministry declined to comment on the status of the report.

Activists say Perhilitan should work harder to relocate problem monkeys, or sterilise troublesome groups. Discussions on sterilisation, which costs nine times more per monkey than culling, according to Perhilitan, have been under way for some time, and a handful of pilot programmes have begun.

Sterilisation has been successful in the high-density cities of Hong Kong and Singapore.

"The conflict between macaques and humans is the one of the biggest threats to the survival of the species," SM Mohd Idris of the animal rights group Sahabat Alam Malaysia wrote in a letter last month to online newspaper Free Malaysia Today. "This should be an essential focus of conservation initiatives if macaques are to have a future in increasingly urbanised environments."

As Susan Lau who lives close to the Kuala Lumpur wildlife sanctuary puts it, "We certainly have a great deal to learn about how to care for our natural environment, as well as the creatures we must learn to share it with."